Search descriptor

Chemically Advanced Template Search descriptors = CATS descriptors substructure descriptors (0 pharmacophore-based descriptors)... 

This virtual search space can be searched using a feature tree descriptor. 

The atom pair, ap, and topological torsion, tt, descriptors are selected for illustrative purposes in the similarity searching context. 

Increasing the fuzziness of object description reduces the number of descriptors used and broadens the scope of a similarity search. At the same time, increasing fuzziness may reduce the discriminatory power of desaiptors to unacceptable levels. Therefore it is desirable to be able to control the degree of fuzziness of desaiptors. 

After an alignment of a set of molecules known to bind to the same receptor a comparative molecular field analysis CoMFA) makes it possible to determine and visuahze molecular interaction regions involved in hgand-receptor binding [51]. Further on, statistical methods such as partial least squares regression PLS) are applied to search for a correlation between CoMFA descriptors and biological activity. The CoMFA descriptors have been one of the most widely used set of descriptors. However, their apex has been reached. 

Multivariate data analysis usually starts with generating a set of spectra and the corresponding chemical structures as a result of a spectrum similarity search in a spectrum database. The peak data are transformed into a set of spectral features and the chemical structures are encoded into molecular descriptors [80]. A spectral feature is a property that can be automatically computed from a mass spectrum. Typical spectral features are the peak intensity at a particular mass/charge value, or logarithmic intensity ratios. The goal of transformation of peak data into spectral features is to obtain descriptors of spectral properties that are more suitable than the original peak list data. 

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

Schuffenhauer A, Gillet VJ, Willett P. Similarity searching in files of 3D chemical structures analysis of the BIOSTER database using 2D fingerprints and molecular field descriptors. J Chem Inf Comput Sci 2000 40 295-307. 

The recent increase of interest in PSA can also be demonstrated by the number of publications mentioning this descriptor over the past 15 years-as counted by the popular scientific search engine Google Scholar [11]. In Fig. 5.2, one can see that until around 1993 the term PSA was practically unused in scientific pubhca-tions, the first increase is visible in the period 1994 to 2001, while in more recent years a very steep increase in the number of publications using this descriptor has been witnessed. 

For (AGh 0), these two regimes are approximately balanced, and a maximum in the exchange current density is predicted. This is the optimal value of the descriptor, and it immediately suggests that a reasonable goal for a computational, combinatorial electrocatalyst search is to find alloys with AGh values close to zero. 

A second example of a VS exercise that was largely fingerprint-based was that of Boecker et al., in search of novel series for dopamine D2 and dopamine D3 blockers [65]. A set of known actives consisting of 472 dopamine D2 and D3 ligands was assembled from the literature. The SPECS database of 230,000 compounds was chosen from which to identify compounds. Two descriptor sets were calculated MOE2D [51] and CATS3D [77] for both query and database molecules. Neighbors... 

On the other hand, there is considerable interest to quantify the similarities between different molecules, in particular, in pharmacology [7], For instance, the search for a new drug may include a comparative analysis of an active molecule with a large molecular library by using combinatorial chemistry. A computational comparison based on the similarity of empirical data (structural parameters, molecular surfaces, thermodynamical data, etc.) is often used as a prescreening. Because the DFT reactivity descriptors measure intrinsic properties of a molecular moiety, they are in fact chemical fingerprints of molecules. These descriptors establish a useful scale of similarity between the members of a large molecular family (see in particular Chapter 15) [18-21],... 

The stability of oxygen-centered radicals has been studied repeatedly in recent years in search of quantitative descriptors of antioxidant activity. The antioxidant activity of phenols is indeed so well correlated with O - H BDEs and the ionization potential that these two energies can be used as the guiding... 

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